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<h3>Transcript Table</h3>

<h4>Top row of buttons</h4>
<table border=0>
<tr><td><i>Buttons</i><td>Description</i>
<tr><td valign="top">Libs <td>Show the table of library counts for the selected transcript(s).
<br>If no SNPs are not covered by reads, its #Libs will be zero.
<tr><td valign="top">Variants<td> Show the table of variants that are found in the selected transcript(s).
<tr><td  valign="top">Exons<td> Show the table of exons that are found in the selected transcript(s).
<tr><td valign="top">Draw<td> Draw the align of transcript exons and variants relative to the parent gene.
<tr><td valign="top">Align<td> Display a pop-up a window with the alignment, where '+' is blossum62 >0,
'x' is blossum62<=0, and '-' is gap.
<tr><td valign="top">Export...
<td>A popup window will display the following:
<ol>
<li>Table of columns - writes the table to file.
<li>Parental proteins - writes (appends) the Ref and Alt proteins to file.
<li>Alignment of parental protein - writes (appends) the Ref/Alt alignment.
<br>Warning: if you select many or allow this to run on all rows in a big table, it will take a long time.
</ol>

<tr><td valign="top">Copy Trans..<td> Copy the transcript name from the selected row so that it can be pasted.
<br>Click with the right mouse button to change it to "Copy identifier..", 
<br>which will copy the Identifier into the clipboard for pasting elsewhere.
</table>

<h4>Column Description</h4>
Most columns are obvious by their names. But the following are a few non-obvious.
<br>Some data is optional, so may not be available.

<br>
<table border=0>
<tr><td><i>Column</i><td>Description</i>
<tr><td valign="top">TRANSid<td>mySQL identifier, used internally
<tr><td valign="top">GENEid<td>mySQL identifier, used internally. This is useful to show what trans belong to the same gene.
<tr><td valign="top">Identifier<td>e.g. Ensembl
<tr><td valign="top">Descript<td>NCBI description (if loaded)
<tr><td valign="top">Rank<td>The transcripts for a gene are ranked according to the number of reads they have, hence,
<br>rank=1 provides the best transcript per gene based on this criteria.
<tr><td valign="top">ATG<td>Start codon.
<tr><td valign="top">Stop<td>End codon.
<tr><td valign="top">5'UTR<td>Distance from the start codon (referred to as ATG).
<br>NOTE: this is ATG-Start, without removing introns within non-coding exons 
<tr><td valign="top">3'UTR<td>Distance from the end_codon (referred to as Stop).
<br>NOTE: this is End-Stop, without removing introns within non-coding exons.

<tr><td valign="top">#Libs<td>Number of libraries with coverage of at least one.
<tr><td valign="top">#LibAI<td>Number of libraries that have AI p-value&lt;0.05.
<br>Use the library selection to view the p-values for all libraries.
<tr><td valign="top">#Read<td>Total number of ref+alt across all libraries.
<tr><td valign="top">#cIndel<td>Number of coding Indels.
<tr><td valign="top">#cSNPs<td>Number of coding SNPs
<tr><td valign="top">#SNPCov<td>Number of SNPs with at least one library with Ref+Alt&gt;=20. 
<tr><td valign="top">#SNPAI<td>Number of SNPs with at least one library with AI p-value&lt;0.05.
<tr><td valign="top">#Mis<td>Number of missense SNPs.
<tr><td valign="top">#Damage<td>What is a 'damaged' SNP depends on where the SNP annotation came from.
<br>For example, it may be an Ensembl Variant Predictor SIFT call, or a snpEFF 'high'.


<tr><td valign="top">Length<td>From Start to End.
<tr><td valign="top">ntLen<td>Spliced transcript length including UTRs (of reference)
<tr><td valign="top">RefProLen<td>Length of the reference protein.
<tr><td valign="top">AltProLen<td>Length of the alternate protein.
<tr><td valign="top">gtkRmk<td>Remarks non-regular coordinates.
<tr><td valign="top">odRmk<td>Remarks opposite direction replicas or SNPs, as follows:
<ol type="a">

<li>odSNP Two or more AI (p-value&lt;0.05) SNPs have opposite direction. 
The 'odSNP:' will be followed by the offending library(s), e.g. odSNP: YfMus.

<br>To view the SNPs:
<ol type="i">
<li>Select the transcript followed by "Variant".
<li>Turn on the RefAlt Ratio and Score columns for the offending library, e.g. YfMus.
<br>You will see that one or more have the opposite direction sign before their ratio,
<br>and the score will be in the opposite direction from 0.5. 
</ol>

<li>odREP The transcript has one or more libs where the summed SNP replicas are in opposite directions.
<br>For example, if there are 4 replicas of (90:120, 100:85, 100:70, 125:75), 
the first would be flagged. 
<br>To see the offending replicas, 
<ol  type="i">
<li>Select the transcript, then select "Libs"; 
<li>From the LibList table, select all libraries followed by "Replica". 
<li>The offending replica(s) will have a value in the "Rep pval" column, all
other entries have "--".
</ol>
</table>


<p><i>Library Group Selection</i>
<ul type="circle">
<li>Select at least one option from each row, then select "Apply Selection".
<li>Ratio=Ref:Alt, Score=Ref/(Ref+Alt), Pval=p-value
</ul>
<p><i>Library Ref:Alt Selection</i>
<ul type="circle">
<li>Individually select libraries for Ratio, Score and/or Pvalue.
</ul>

<h4>Manipulating the table</h4>
<ol>
<li>Columns can be moved around by selecting a column heading and moving it.
<li>Columns can be sorted by right click (descending); left click or second right click (ascending).
<li>Various columns can be turned on or off by selecting <i>Columns: Select</i> and setting the desired 
column appropriately. 
<li>When a new table is generated, it uses the last selected column settings. However, the order
of columns is not preserved for new tables.
</ol>

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